RNA 3D Hub

JAR3D Query RF02032-CCF-3.98 completed
Run on Motif Atlas Version using the Rfam secondary structure. Run with the CaCoFold secondary structure.

Rfam family RF02032 maps to these 73 chains: 9L0R|1|A, 9L0R|1|B, 9L0R|1|C, 9L0R|1|D, 9L0R|1|E, 9L0R|1|F, 9L0R|1|G, 9L0R|1|H, 9L0R|1|I, 9L0R|1|J, 9L0R|1|K, 9L0R|1|L, 9LEC|1|J, 9LEE|1|A, 9LEE|1|B, 9LEE|1|C, 9LEE|1|D, 9LEE|1|E, 9LEE|1|F, 9LEE|1|G, 9LEE|1|H, 9LEE|1|I, 9LEE|1|J, 9LEL|1|J, 9LEM|1|A, 9LEM|1|B, 9LEM|1|C, 9LEM|1|D, 9LEM|1|E, 9LEM|1|F, 9LEM|1|G, 9LEM|1|H, 9LEM|1|I, 9LEM|1|J, 9LHK|1|G, 9LHL|1|A, 9LHL|1|B, 9LHL|1|C, 9LHL|1|D, 9LHL|1|E, 9LHL|1|F, 9LHL|1|G, 9LHL|1|H, 9LHL|1|I, 9LHL|1|J, 9LHL|1|K, 9LHL|1|L, 9LHL|1|M, 9LHL|1|N, 9LMF|1|A, 9LMF|1|B, 9LMF|1|C, 9LMF|1|D, 9LMF|1|E, 9LMF|1|F, 9LMF|1|G, 9LMF|1|H, 9LMF|1|I, 9LMF|1|J, 9MEE|1|A, 9MEE|1|B, 9MEE|1|C, 9MEE|1|D, 9MEE|1|E, 9MEE|1|F, 9MEE|1|G, 9MEE|1|H, 9MEE|1|I, 9MEE|1|J, 9MEE|1|K, 9MEE|1|L, 9MEE|1|M, 9MEE|1|N See more about them at RNA 3D Hub by filtering on the chain or the Rfam family.

Loop 21 3-way junction loop

Column numbers: 488-490, 524-534, 580-585 - View nucleotides in PDB file(s) 
    Scored sequences and counts

    
    UAC*GUG-GACA-AG*CAAAAG    4

    
    UAC*GUG-GAUA-GG*CUAAAG    3

    
    UAC*GUG-GACAAUG*CGAAAG    2

    
    UAC*GUG-GAAA-CG*CCAAAG    2

    
    UAC*GUG-GAAA-UC*GUAAAG    2

    
    UAC*GUG-GAUA-AG*CAAAAG    2

    
    UAC*GUG-GAUA-CG*CAAAAG    2

    
    GAC*GUG-GAUG-UC*G--AGG    2

    
    UAC*GUGUGUGUAAA*UAAAAU    1

    
    UAC*GUG-GACAAAA*UCAAAG    1

    
    GAC*GUG-GAUA-AG*CAAAGG    1

    
    UAC*GUG-GAAA-AU*AGAAAG    1

    
    UAC*GUG-GAAA-CA*UUAAAG    1

    
    UAC*GUG-GAAA-CG*CUAAAG    1

    
    UAC*GUG-GAAA-CG*UAAAAG    1

    
    UAC*GUG-GAAA-CG*UCAAAG    1

    
    UAC*GUG-GAAA-CG*UUAAAG    1

    
    UAC*GUG-GACA-AA*GCAAAG    1

    
    UAC*GUG-GACA-AG*CGAGAG    1

    
    UAC*GUG-GACA-CG*CAAAAG    1

    
    UAC*GUG-GAUA-AA*UGAAAG    1

    
    UAC*GUG-GAUA-CA*CUAAAG    1

    
    UAC*GUG-GAUA-UU*AUAAAG    1

    
    UUC*GAG-GAUA-AG*CGAAAG    1
Click on headings to reorder table
# Matching motif group Acceptance Rate Mean Cutoff Score Full Edit Distance Interior Edit Distance Basepair Diagram and most common annotation
1

Motif group J3_45941.1

Basepair signature:
13

0.00 -72.42 14 9

2

Motif group J3_88257.1

Basepair signature:
14

0.00 -84.09 13 8

3

Motif group J3_58957.1

Basepair signature:
17

0.00 -84.60 13 9

4

Motif group J3_83726.1

Basepair signature:
17

0.00 -90.79 8 7

5

Motif group J3_00210.1

Basepair signature:
16

0.00 -94.66 12 8

6

Motif group J3_32030.1

Basepair signature:
15

0.00 -97.82 10 7

7

Motif group J3_45099.1

Basepair signature:
19

0.00 -107.52 11 7

8

Motif group J3_71753.1

Basepair signature:
17

0.00 -111.03 12 9

9

Motif group J3_38881.1

Basepair signature:
19

0.00 -114.39 11 7

10

Motif group J3_62630.1

Basepair signature:
12

0.00 -115.94 14 9

11

Motif group J3_53439.1

Basepair signature:
16

0.00 -116.92 13 8

12

Motif group J3_45482.1

Basepair signature:
16

0.00 -117.18 13 8

13

Motif group J3_65990.1

Basepair signature:
14

0.00 -124.44 11 7

14

Motif group J3_69441.1

Basepair signature:
14

0.00 -127.32 13 9

15

Motif group J3_76475.2

Basepair signature:
16

0.00 -130.86 11 9

16

Motif group J3_96372.2

Basepair signature:
16

0.00 -133.66 9 8

17

Motif group J3_44792.1

Basepair signature:
19

0.00 -135.80 13 9

18

Motif group J3_23373.1

Basepair signature:
17

0.00 -141.68 11 9

19

Motif group J3_94999.1

Basepair signature:
12

0.00 -141.68 9 7

20

Motif group J3_41596.1

Basepair signature:
17

0.00 -143.55 11 10

21

Motif group J3_20992.1

Basepair signature:
18

0.00 -145.32 13 9

22

Motif group J3_98484.1

Basepair signature:
16

0.00 -148.25 13 10

23

Motif group J3_34864.2

Basepair signature:
15

0.00 -148.81 11 8

24

Motif group J3_19286.1

Basepair signature:
15

0.00 -150.96 11 8

25

Motif group J3_46299.2

Basepair signature:
19

0.00 -155.27 13 9

26

Motif group J3_07703.1

Basepair signature:
16

0.00 -159.59 11 7

27

Motif group J3_98379.3

Basepair signature:
16

0.00 -161.54 12 6

28

Motif group J3_72012.1

Basepair signature:
16

0.00 -162.72 12 9

29

Motif group J3_99563.1

Basepair signature:
17

0.00 -164.41 13 9

30

Motif group J3_12393.2

Basepair signature:
13

0.00 -164.58 9 8

31

Motif group J3_22899.1

Basepair signature:
20

0.00 -164.58 15 11

32

Motif group J3_64189.2

Basepair signature:
11

0.00 -169.49 11 8

33

Motif group J3_75408.1

Basepair signature:
20

0.00 -171.98 12 10

34

Motif group J3_59706.1

Basepair signature:
21

0.00 -176.20 13 10

35

Motif group J3_89095.1

Basepair signature:
13

0.00 -177.86 11 9

36

Motif group J3_20574.1

Basepair signature:
14

0.00 -178.13 8 7

37

Motif group J3_76375.1

Basepair signature:
17

0.00 -180.80 13 11

38

Motif group J3_04521.1

Basepair signature:
10

0.00 -182.17 10 7

39

Motif group J3_68164.1

Basepair signature:
15

0.00 -183.32 10 7

40

Motif group J3_31965.2

Basepair signature:
13

0.00 -186.89 10 7

41

Motif group J3_64069.1

Basepair signature:
13

0.00 -187.41 11 7

42

Motif group J3_32857.1

Basepair signature:
15

0.00 -188.41 13 9

43

Motif group J3_00458.1

Basepair signature:
20

0.00 -188.68 15 11

44

Motif group J3_32601.5

Basepair signature:
12

0.00 -188.72 11 7

45

Motif group J3_25303.4

Basepair signature:
19

0.00 -189.30 12 8

46

Motif group J3_89368.5

Basepair signature:
13

0.00 -190.98 10 7

47

Motif group J3_41339.1

Basepair signature:
20

0.00 -191.03 13 11

48

Motif group J3_87797.1

Basepair signature:
15

0.00 -191.35 13 8

49

Motif group J3_04315.1

Basepair signature:
20

0.00 -192.85 14 11

50

Motif group J3_15893.1

Basepair signature:
14

0.00 -195.46 11 8

C-di-AMP riboswitch

51

Motif group J3_28621.5

Basepair signature:
13

0.00 -196.13 10 7

52

Motif group J3_97642.1

Basepair signature:
13

0.00 -197.89 10 7

53

Motif group J3_46173.1

Basepair signature:
16

0.00 -198.31 15 12

54

Motif group J3_39320.1

Basepair signature:
21

0.00 -198.54 15 12

55

Motif group J3_97609.1

Basepair signature:
15

0.00 -199.75 15 10

56

Motif group J3_24127.1

Basepair signature:
13

0.00 -200.36 8 7

57

Motif group J3_47707.1

Basepair signature:
20

0.00 -201.08 16 11

58

Motif group J3_33494.1

Basepair signature:
12

0.00 -202.39 10 8

59

Motif group J3_82572.1

Basepair signature:
11

0.00 -202.82 11 8

60

Motif group J3_84052.1

Basepair signature:
17

0.00 -205.91 15 10

61

Motif group J3_77951.1

Basepair signature:
20

0.00 -207.54 13 10

62

Motif group J3_05216.1

Basepair signature:
12

0.00 -207.75 8 7

63

Motif group J3_83592.1

Basepair signature:
19

0.00 -208.17 13 10

64

Motif group J3_83332.1

Basepair signature:
13

0.00 -209.90 11 10

65

Motif group J3_61367.1

Basepair signature:
23

0.00 -213.54 15 13

66

Motif group J3_01052.1

Basepair signature:
13

0.00 -213.78 11 9

67

Motif group J3_36387.1

Basepair signature:
16

0.00 -213.79 13 9

68

Motif group J3_44163.2

Basepair signature:
18

0.00 -213.90 12 9

69

Motif group J3_21426.1

Basepair signature:
19

0.00 -215.88 14 10

70

Motif group J3_35667.2

Basepair signature:
12

0.00 -216.30 11 8

71

Motif group J3_01596.1

Basepair signature:
23

0.00 -221.51 16 12

72

Motif group J3_89044.1

Basepair signature:
15

0.00 -224.92 12 8

73

Motif group J3_76911.2

Basepair signature:
11

0.00 -225.32 9 7

74

Motif group J3_06335.1

Basepair signature:
14

0.00 -226.38 13 8

75

Motif group J3_44961.1

Basepair signature:
16

0.00 -227.66 15 11

76

Motif group J3_65403.1

Basepair signature:
21

0.00 -228.52 14 11

77

Motif group J3_21998.1

Basepair signature:
14

0.00 -229.13 12 8

78

Motif group J3_58525.1

Basepair signature:
20

0.00 -232.22 15 12

79

Motif group J3_36821.1

Basepair signature:
11

0.00 -232.93 12 7

80

Motif group J3_85054.4

Basepair signature:
14

0.00 -233.72 10 8

81

Motif group J3_88233.1

Basepair signature:
15

0.00 -236.00 12 10

82

Motif group J3_20650.1

Basepair signature:
13

0.00 -238.41 13 9

83

Motif group J3_08394.3

Basepair signature:
20

0.00 -241.11 13 11

84

Motif group J3_89737.1

Basepair signature:
14

0.00 -241.59 14 12

5S rRNA junction

85

Motif group J3_55773.1

Basepair signature:
15

0.00 -242.58 11 10

86

Motif group J3_92705.1

Basepair signature:
12

0.00 -244.85 9 7

87

Motif group J3_51910.1

Basepair signature:
12

0.00 -245.46 13 8

88

Motif group J3_46317.4

Basepair signature:
19

0.00 -248.81 13 9

89

Motif group J3_47324.1

Basepair signature:
10

0.00 -251.30 12 10

90

Motif group J3_98798.1

Basepair signature:
13

0.00 -253.86 9 9

91

Motif group J3_71677.1

Basepair signature:
13

0.00 -257.95 13 8

92

Motif group J3_36499.1

Basepair signature:
13

0.00 -259.05 12 9

93

Motif group J3_17385.4

Basepair signature:
12

0.00 -259.27 11 9

94

Motif group J3_37047.6

Basepair signature:
15

0.00 -259.46 15 11

95

Motif group J3_19545.2

Basepair signature:
12

0.00 -262.71 11 8

96

Motif group J3_32852.6

Basepair signature:
12

0.00 -269.33 10 7

97

Motif group J3_37089.1

Basepair signature:
12

0.00 -272.93 12 8

98

Motif group J3_44724.7

Basepair signature:
12

0.00 -273.60 11 7

99

Motif group J3_19664.1

Basepair signature:
22

0.00 -276.68 17 14

100

Motif group J3_11934.4

Basepair signature:
13

0.00 -278.42 11 9

101

Motif group J3_22198.1

Basepair signature:
12

0.00 -279.63 13 8

102

Motif group J3_83516.4

Basepair signature:
22

0.00 -280.69 19 14

103

Motif group J3_28639.1

Basepair signature:
18

0.00 -284.09 16 14

104

Motif group J3_38098.1

Basepair signature:
25

0.00 -284.17 18 14

105

Motif group J3_51249.1

Basepair signature:
13

0.00 -284.58 10 9

106

Motif group J3_46124.1

Basepair signature:
26

0.00 -289.23 16 14

107

Motif group J3_93637.1

Basepair signature:
15

0.00 -290.76 11 10

108

Motif group J3_61124.2

Basepair signature:
10

0.00 -292.07 10 8

109

Motif group J3_03190.1

Basepair signature:
17

0.00 -300.55 18 17

110

Motif group J3_93059.1

Basepair signature:
13

0.00 -308.96 13 8

111

Motif group J3_72575.1

Basepair signature:
13

0.00 -309.11 15 10

112

Motif group J3_93261.1

Basepair signature:
25

0.00 -309.18 18 16

113

Motif group J3_97280.1

Basepair signature:
19

0.00 -309.21 13 10

114

Motif group J3_58090.1

Basepair signature:
13

0.00 -311.94 15 11

115

Motif group J3_31041.1

Basepair signature:
12

0.00 -315.75 13 9

116

Motif group J3_69466.1

Basepair signature:
27

0.00 -318.23 18 16

117

Motif group J3_28315.1

Basepair signature:
12

0.00 -318.98 13 8

118

Motif group J3_76043.3

Basepair signature:
11

0.00 -320.40 11 9

119

Motif group J3_80708.1

Basepair signature:
12

0.00 -328.49 13 8

120

Motif group J3_70599.1

Basepair signature:
11

0.00 -330.75 10 8

121

Motif group J3_67856.4

Basepair signature:
12

0.00 -332.33 11 8

122

Motif group J3_60031.2

Basepair signature:
12

0.00 -333.15 10 7

123

Motif group J3_94652.1

Basepair signature:
10

0.00 -344.72 13 9

124

Motif group J3_30040.2

Basepair signature:
24

0.00 -346.39 14 11

125

Motif group J3_97971.2

Basepair signature:
14

0.00 -347.85 11 10

126

Motif group J3_47376.1

Basepair signature:
10

0.00 -348.80 13 9

127

Motif group J3_63687.1

Basepair signature:
17

0.00 -350.16 17 15

128

Motif group J3_10118.1

Basepair signature:
7

0.00 -352.16 11 8

129

Motif group J3_09667.1

Basepair signature:
11

0.00 -355.00 11 9

130

Motif group J3_81015.1

Basepair signature:
11

0.00 -356.71 12 8

131

Motif group J3_79369.1

Basepair signature:
10

0.00 -389.39 12 9

132

Motif group J3_52655.4

Basepair signature:
11

0.00 -395.57 10 9

133

Motif group J3_80578.1

Basepair signature:
10

0.00 -418.64 10 8

134

Motif group J3_58429.1

Basepair signature:
27

0.00 -432.04 21 18

135

Motif group J3_26675.1

Basepair signature:
9

0.00 -439.80 13 11

136

Motif group J3_25217.1

Basepair signature:
9

0.00 -454.33 13 10

137

Motif group J3_41097.1

Basepair signature:
9

0.00 -454.48 15 11

phi29 pRNA

138

Motif group J3_28460.1

Basepair signature:
28

0.00 -464.49 23 21

139

Motif group J3_01425.1

Basepair signature:
9

0.00 -469.95 15 11

140

Motif group J3_68440.1

Basepair signature:
19

0.00 -476.54 15 14

141

Motif group J3_82365.4

Basepair signature:
9

0.00 -481.43 11 9

142

Motif group J3_38151.1

Basepair signature:
10

0.00 -483.21 11 8

143

Motif group J3_90186.1

Basepair signature:
20

0.00 -490.79 14 12

144

Motif group J3_14360.1

Basepair signature:
10

0.00 -495.63 13 8

145

Motif group J3_17791.2

Basepair signature:
19

0.00 -499.77 13 10

146

Motif group J3_65214.1

Basepair signature:
28

0.00 -525.46 19 14

147

Motif group J3_75076.1

Basepair signature:
34

0.00 -525.64 25 21

148

Motif group J3_12003.2

Basepair signature:
9

0.00 -551.89 12 9

149

Motif group J3_08040.1

Basepair signature:
29

0.00 -551.90 21 19

150

Motif group J3_59914.1

Basepair signature:
9

0.00 -572.88 12 9

151

Motif group J3_11375.2

Basepair signature:
10

0.00 -574.15 12 9

152

Motif group J3_41486.2

Basepair signature:
8

0.00 -592.40 13 11

153

Motif group J3_74474.1

Basepair signature:
23

0.00 -617.52 21 20

154

Motif group J3_56052.5

Basepair signature:
8

0.00 -652.83 12 10

155

Motif group J3_13378.1

Basepair signature:
38

0.00 -653.60 27 26

156

Motif group J3_08158.1

Basepair signature:
36

0.00 -668.87 29 28

157

Motif group J3_10708.1

Basepair signature:
22

0.00 -681.83 19 17

158

Motif group J3_33327.1

Basepair signature:
26

0.00 -717.97 22 20

159

Motif group J3_99595.1

Basepair signature:
9

0.00 -762.03 12 10

160

Motif group J3_24879.1

Basepair signature:
28

0.00 -788.93 19 16

161

Motif group J3_07845.1

Basepair signature:
7

0.00 -820.94 13 11

162

Motif group J3_75962.2

Basepair signature:
9

0.00 -852.73 12 9

163

Motif group J3_92134.2

Basepair signature:
26

0.00 -857.60 17 14

164

Motif group J3_30104.1

Basepair signature:
8

0.00 -889.74 15 11

165

Motif group J3_30478.1

Basepair signature:
8

0.00 -900.92 14 11

Coloring options: